—
—
—
—
—

              
# $Id: TermAdaptorDriver.pm,v 1.5 2006/07/04 22:23:12 mauricio Exp $
#
# BioPerl module for Bio::DB::BioSQL::Oracle::TermAdaptorDriver
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
# 
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
HideShow 46 lines of Pod
=head1 NAME
Bio::DB::BioSQL::Oracle::TermAdaptorDriver - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::Oracle::TermAdaptorDriver;
use vars qw(@ISA);
use strict;
use Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver;
@ISA = qw(Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver);
HideShow 16 lines of Pod
=head2 remove_synonyms
 Title   : remove_synonyms
 Usage   :
 Function: Removes all synonyms for an ontology term.
 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The calling persistence adaptor.
           The persistent term object for which to remove the synonyms
           (a Bio::DB::PersistentObjectI compliant object with defined
           primary key).
=cut
sub remove_synonyms{
    my ($self,$adp,$obj) = @_;
    # delete statement cached?
    my $cachekey = "DELETE SYNONYMS";
    my $sth = $adp->sth($cachekey);
    # if not we need to build it
    if(! $sth) {
        # we need table name and foreign key
        my $table = $self->table_name("TermSynonym");
        my $fkname = $self->foreign_key_name($obj->obj);
        # build, prepare, and cache the SQL statement
        $sth = $self->_build_sth($adp, $cachekey,
                                 "DELETE FROM $table WHERE $fkname = ?");
    }
    # bind parameters and execute insert
    my $dbgmsg = "executing with values (".
        $obj->primary_key().") (FK to ".ref($obj->obj).")";
    $adp->debug("$cachekey: $dbgmsg\n");
    my $rv = $sth->execute($obj->primary_key());
    if(! $rv) {
        $self->warn("failed to remove term synonyms (".ref($adp)
                    .") with values (".$obj->primary_key()
                    .") (FK to ".ref($obj->obj)."):\n".$sth->errstr());
    }
    return $rv;
}
HideShow 18 lines of Pod
=head2 store_synonym
 Title   : store_synonym
 Usage   :
 Function: Stores a synonym for an ontology term.
 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The calling persistence adaptor.
           The persistent term object for which to store the synonym
           (a Bio::DB::PersistentObjectI compliant object with defined
           primary key).
           The synonym to store (a scalar). 
=cut
sub store_synonym{
    my ($self,$adp,$obj,$syn) = @_;
    # insert and look-up statements cached?
    my $icachekey = "INSERT SYNONYM";
    my $isth = $adp->sth($icachekey);
    # if not we need to build them
    if(! $isth) {
        # we need table name, foreign key, and slot map
        my $table = $self->table_name("TermSynonym");
        my $fkname = $self->foreign_key_name($obj->obj);
        my $colmap = $self->slot_attribute_map($table);
        # build, prepare, and cache the SQL statements
        $isth = $self->_build_sth($adp, $icachekey,
                                  "INSERT INTO $table (".
                                  join(", ", $colmap->{'synonym'}, $fkname).
                                  ") VALUES (?, ?)");
    }
    # bind parameters and execute insert
    my $dbgmsg = "executing with values ($syn, ".
        $obj->primary_key().") (synonym, FK to ".ref($obj->obj).")";
    $adp->debug("$icachekey: $dbgmsg\n");
    my $rv = $isth->execute($syn, $obj->primary_key());
    if(! $rv) {
        # this might be a UK failure, not a bad statement error
        if (index($isth->errstr(), "ORA-00001") >= 0) {
            # we actually don't need to execute a look-up here because the
            # synonym is not an object and hence has no primary key itself
            $rv = "0E0"; # evaluates to TRUE, but numerically equals zero
        } else {
            $self->warn("failed to store term synonym (".ref($adp)
                        .") with values ($syn) (FK ".$obj->primary_key()
                        ." to ".ref($obj->obj)."):\n"
                        .$isth->errstr());
        }
    }
    return $rv;
}
sub _build_sth{
    my ($self,$adp,$cachekey,$sql) = @_;
    # prepare and cache
    $adp->debug("$cachekey: preparing: $sql\n");
    my $sth = $adp->dbh->prepare($sql);
    $self->throw("failed to prepare \"$sql\": ".$adp->dbh->errstr)
        unless $sth;
    $adp->sth($cachekey,$sth);
    return $sth;
}
HideShow 17 lines of Pod
=head2 get_synonyms
 Title   : get_synonyms
 Usage   :
 Function: Retrieves the synonyms for an ontology term and adds them
           the term's synonyms.
 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The calling persistence adaptor.
           The persistent term object for which to retrieve the
           synonyms (a Bio::DB::PersistentObjectI compliant object
           with defined primary key).
=cut
sub get_synonyms{
    my ($self,$adp,$obj) = @_;
    # look-up statement cached?
    my $cachekey = "SELECT SYNONYMS";
    my $sth = $adp->sth($cachekey);
    # if not we need to build it
    if(! $sth) {
        # we need table name, foreign key, and slot map
        my $table = $self->table_name("TermSynonym");
        my $fkname = $self->foreign_key_name($obj->obj);
        my $colmap = $self->slot_attribute_map($table);
        # build, prepare, and cache the SQL statement
        $sth = $self->_build_sth($adp, $cachekey,
                                 "SELECT ".$colmap->{'synonym'}.
                                 " FROM $table WHERE $fkname = ?");
    }
    # bind parameters and execute select
    my $dbgmsg = "executing with values (".
        $obj->primary_key().") (FK to ".ref($obj->obj).")";
    $adp->debug("$cachekey: $dbgmsg\n");
    my $rv = $sth->execute($obj->primary_key());
    $self->warn("failed to execute $cachekey: ".$sth->errstr) unless $rv;
    while(my $row = $sth->fetchrow_arrayref()) {
        $obj->add_synonym($row->[0]);
    }
    return $rv;
}
HideShow 21 lines of Pod
=head2 bind_param
 Title   : bind_param
 Usage   :
 Function: Binds a parameter value to a prepared statement.
           We override this in order to possibly truncate term
           definitions longer than 4000 characters, the limit of
           Oracle's VARCHAR2 data type. Note that this problem does
           not exist with Pg's and mysql's text types.
 Example :
 Returns : the return value of the DBI::bind_param() call
 Args    : the DBI statement handle to bind to
           the index of the column (1-based)
           the value to bind
           additional arguments to be passed to the sth->bind_param call
=cut
sub bind_param{
    my ($self,$sth,$i,$val,@bindargs) = @_;
     
    # definition is the 3rd value to bind
    if (($i == 3) && defined($val) && (length($val) > 4000)) {
        $self->warn("term definition is "
                    .length($val)." chars long, need to truncate to 4000");
        $val = substr($val,0,4000);
    }
    return $self->SUPER::bind_param($sth,$i,$val,@bindargs);
}
1;